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tsa_pH <-
merge_TSA(raw_data_path =
c("/Users/billy/Desktop/SGS_Lab/TSA/TSAR_Files/CAFL_pH_20211203_20211203_162735_RawData_CAFL_pH_TSA_20211203.eds.txt",
"/Users/billy/Desktop/SGS_Lab/TSA/TSAR_Files/CAFL_pH_3_20211206_162845_RawData_CAFL_pH_3.eds.txt"),
analysis_file_path =
c("/Users/billy/Desktop/SGS_Lab/TSA/TSAR_Files/CAFL_pH_20211203_20211203_162735_AnalysisResults.txt",
"/Users/billy/Desktop/SGS_Lab/TSA/TSAR_Files/CAFL_pH_3_20211206_162845_AnalysisResults.txt"))
head(tsa_pH)
## well_ID Well Protein Ligand Tm dTm D
## 1 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 2 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 3 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 4 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 5 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 6 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## Analysis Group Flags Experiment File Name condition_ID Well.Position
## 1 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 2 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 3 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 4 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 5 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 6 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## Temperature Fluorescence
## 1 86.14173 200369.2
## 2 86.26060 199525.2
## 3 86.32003 199102.9
## 4 86.37946 198680.3
## 5 86.20116 199947.3
## 6 86.49833 197835.2
To get the ID:
condition_IDs(tsa_pH)
## [1] "CA FL_Tris (pH 8)" "CA FL_Tris (pH 6.8)" "CA FL_Tris (pH 4)"
## [4] "CA FL_NaP (pH 8)" "Buffer_Tris (pH 8)" "Buffer_Tris (pH 6.8)"
## [7] "Buffer_Tris (pH 4)" "Buffer_NaP (pH 8)"
control_ID <- "CA FL_Tris (pH 8)"
TSA_Tms(tsa_pH)
## condition_ID Avg_Tm SD_Tm Tm_ 1 Tm_ 2 Tm_ 3 Tm_ 4
## 1 CA FL_Tris (pH 8) 53.13616 0.09486345 53.13263 53.13263 52.98625 53.28607
## 2 CA FL_Tris (pH 6.8) 53.30693 0.11118899 53.13263 53.27901 53.42539 53.28607
## 3 CA FL_Tris (pH 4) 56.01484 0.24237114 55.76747 55.91385 55.76747 56.06704
## 4 CA FL_NaP (pH 8) 52.08727 7.39342995 54.45005 54.74281 54.88919 37.03931
## 5 Buffer_Tris (pH 8) 56.06023 45.74976773 NA 23.71026 88.41020 NA
## 6 Buffer_Tris (pH 6.8) 75.60417 26.06299696 92.21608 87.38554 24.29578 73.48473
## 7 Buffer_Tris (pH 4) 76.46719 29.50544327 24.00302 88.84934 92.65522 92.21973
## 8 Buffer_NaP (pH 8) 48.59927 30.71310609 NA NA 29.41908 NA
## Tm_ 5 Tm_ 6 Protein Ligand
## 1 53.13970 53.13970 CA FL Tris (pH 8)
## 2 53.43243 53.28607 CA FL Tris (pH 6.8)
## 3 56.35978 56.21341 CA FL Tris (pH 4)
## 4 55.33521 56.06704 CA FL NaP (pH 8)
## 5 NA NA Buffer Tris (pH 8)
## 6 92.07336 84.16953 Buffer Tris (pH 6.8)
## 7 NA 84.60864 Buffer Tris (pH 4)
## 8 84.02316 32.35556 Buffer NaP (pH 8)
TSA_boxplot(tsa_pH,
control = control_ID)
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TSA_boxplot(tsa_pH,
control = control_ID,
color_by = "Ligand")
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Normalize curves
normalized_tsa_pH <- normalize_fluorescence(tsa_data = tsa_pH)
head(normalized_tsa_pH)
## well_ID Well Protein Ligand Tm dTm D
## 1 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 2 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 3 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 4 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 5 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## 6 A01_CAFL_pH_TSA_20211203.eds A01 CA FL Tris (pH 8) 53.13263 <NA>
## Analysis Group Flags Experiment File Name condition_ID Well.Position
## 1 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 2 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 3 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 4 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 5 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## 6 AG 1 2 CAFL_pH_TSA_20211203.eds CA FL_Tris (pH 8) A01
## Temperature Fluorescence RFU
## 1 86.14173 200369.2 0.1582415
## 2 86.26060 199525.2 0.1562010
## 3 86.32003 199102.9 0.1551799
## 4 86.37946 198680.3 0.1541584
## 5 86.20116 199947.3 0.1572215
## 6 86.49833 197835.2 0.1521150
for(i in 1:condition_IDs(normalized_tsa_pH, n = TRUE)) {
cond_i <- condition_IDs(normalized_tsa_pH)[i]
subset_i <- normalized_tsa_pH$condition_ID == cond_i
subset_i <- normalized_tsa_pH[subset_i, ]
plot_i <- TSA_wells_plot(subset_i)
print(plot_i)
}
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Normalized Data
tsa_compare_plot(normalized_tsa_pH,
y = "RFU",
control_condition = control_ID)
## $`CA FL_Tris (pH 6.8)`
##
## $`CA FL_Tris (pH 4)`
##
## $`CA FL_NaP (pH 8)`
##
## $`Buffer_Tris (pH 8)`
##
## $`Buffer_Tris (pH 6.8)`
##
## $`Buffer_Tris (pH 4)`
##
## $`Buffer_NaP (pH 8)`
##
## $`Control: CA FL_Tris (pH 8)`
Original Data
tsa_compare_plot(normalized_tsa_pH,
y = "Fluorescence",
control_condition = control_ID)
## $`CA FL_Tris (pH 6.8)`
##
## $`CA FL_Tris (pH 4)`
##
## $`CA FL_NaP (pH 8)`
##
## $`Buffer_Tris (pH 8)`
##
## $`Buffer_Tris (pH 6.8)`
##
## $`Buffer_Tris (pH 4)`
##
## $`Buffer_NaP (pH 8)`
##
## $`Control: CA FL_Tris (pH 8)`
# -- Condition IDs
condition_IDs(normalized_tsa_pH)
## [1] "CA FL_Tris (pH 8)" "CA FL_Tris (pH 6.8)" "CA FL_Tris (pH 4)"
## [4] "CA FL_NaP (pH 8)" "Buffer_Tris (pH 8)" "Buffer_Tris (pH 6.8)"
## [7] "Buffer_Tris (pH 4)" "Buffer_NaP (pH 8)"
# -- Well IDs
well_IDs(normalized_tsa_pH)
## [1] "A01_CAFL_pH_TSA_20211203.eds" "A02_CAFL_pH_TSA_20211203.eds"
## [3] "A03_CAFL_pH_TSA_20211203.eds" "A04_CAFL_pH_TSA_20211203.eds"
## [5] "A05_CAFL_pH_TSA_20211203.eds" "A06_CAFL_pH_TSA_20211203.eds"
## [7] "A07_CAFL_pH_TSA_20211203.eds" "A08_CAFL_pH_TSA_20211203.eds"
## [9] "A09_CAFL_pH_TSA_20211203.eds" "A10_CAFL_pH_TSA_20211203.eds"
## [11] "A11_CAFL_pH_TSA_20211203.eds" "A12_CAFL_pH_TSA_20211203.eds"
## [13] "B01_CAFL_pH_TSA_20211203.eds" "B02_CAFL_pH_TSA_20211203.eds"
## [15] "B03_CAFL_pH_TSA_20211203.eds" "B04_CAFL_pH_TSA_20211203.eds"
## [17] "B05_CAFL_pH_TSA_20211203.eds" "B06_CAFL_pH_TSA_20211203.eds"
## [19] "B07_CAFL_pH_TSA_20211203.eds" "B08_CAFL_pH_TSA_20211203.eds"
## [21] "B09_CAFL_pH_TSA_20211203.eds" "B10_CAFL_pH_TSA_20211203.eds"
## [23] "B11_CAFL_pH_TSA_20211203.eds" "B12_CAFL_pH_TSA_20211203.eds"
## [25] "A01_CAFL_pH_3.eds" "A02_CAFL_pH_3.eds"
## [27] "A03_CAFL_pH_3.eds" "A04_CAFL_pH_3.eds"
## [29] "A05_CAFL_pH_3.eds" "A06_CAFL_pH_3.eds"
## [31] "A07_CAFL_pH_3.eds" "A08_CAFL_pH_3.eds"
## [33] "A09_CAFL_pH_3.eds" "A10_CAFL_pH_3.eds"
## [35] "A11_CAFL_pH_3.eds" "A12_CAFL_pH_3.eds"
## [37] "B01_CAFL_pH_3.eds" "B02_CAFL_pH_3.eds"
## [39] "B03_CAFL_pH_3.eds" "B04_CAFL_pH_3.eds"
## [41] "B05_CAFL_pH_3.eds" "B06_CAFL_pH_3.eds"
## [43] "B07_CAFL_pH_3.eds" "B08_CAFL_pH_3.eds"
## [45] "B09_CAFL_pH_3.eds" "B10_CAFL_pH_3.eds"
## [47] "B11_CAFL_pH_3.eds" "B12_CAFL_pH_3.eds"
# -- Proteins Tested
TSA_proteins(normalized_tsa_pH)
## [1] "CA FL" "Buffer"
# -- Ligands Tested
TSA_ligands(normalized_tsa_pH)
## [1] "Tris (pH 8)" "Tris (pH 6.8)" "Tris (pH 4)" "NaP (pH 8)"